ALBERT

Description: Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

Description: 4-Coumarate:CoA ligase (4CL) genes are critical for the biosynthesis of plant phenylpropanoids. Here we identified 20 4CL genes in the genomes of two desert poplars (Populus euphratica and P. pruinosa) and salt-sensitive congener (P. trichocarpa), but 12 in Salix suchowensis (Salix willow). Phylogenetic analyses clustered all Salicaceae 4CL genes into two clades, and one of them (corresponding to the 4CL-like clade from Arabidopsis) showed signals of adaptive evolution, with more genes retained in Populus than Salix and Arabidopsis. We also found that 4CL12 (in 4CL-like clade) showed positive selection along the two desert poplar lineages. Transcriptional profiling analyses indicated that the expression of 4CL2, 4CL11, and 4CL12 changed significantly in one or both desert poplars in response to salt stress compared to that of in P. trichocarpa. Our results suggest that the evolution of the 4CL genes may have contributed to the development of salt tolerance in the two desert poplars.

Description: Genes, Vol. 9, Pages 403: Habitat Fragmentation Reduces Genetic Diversity and Connectivity of the Mexican Spotted Owl: A Simulation Study Using Empirical Resistance Models Genes doi: 10.3390/genes9080403 Authors: Ho Yi Wan Samuel A. Cushman Joseph L. Ganey We evaluated how differences between two empirical resistance models for the same geographic area affected predictions of gene flow processes and genetic diversity for the Mexican spotted owl (Strix occidentalis lucida). The two resistance models represented the landscape under low- and high-fragmentation parameters. Under low fragmentation, the landscape had larger but highly concentrated habitat patches, whereas under high fragmentation, the landscape had smaller habitat patches that scattered across a broader area. Overall habitat amount differed little between resistance models. We tested eight scenarios reflecting a factorial design of three factors: resistance model (low vs. high fragmentation), isolation hypothesis (isolation-by-distance, IBD, vs. isolation-by-resistance, IBR), and dispersal limit of species (200 km vs. 300 km). Higher dispersal limit generally had a positive but small influence on genetic diversity. Genetic distance increased with both geographic distance and landscape resistance, but landscape resistance displayed a stronger influence. Connectivity was positively related to genetic diversity under IBR but was less important under IBD. Fragmentation had a strong negative influence on the spatial patterns of genetic diversity and effective population size (Ns). Despite habitats being more concentrated and less widely distributed, the low-fragmentation landscape had greater genetic diversity than the high-fragmentation landscape, suggesting that highly concentrated but larger habitat patches may provide a genetic refuge for the Mexican spotted owl.

Description: The basic helix-loop-helix (bHLH) transcription factors in insects play essential roles in multiple developmental processes including neurogenesis, sterol metabolism, circadian rhythms, organogenesis and formation of olfactory sensory neurons. The identification and function analysis of bHLH family members of the most destructive insect pest of rice, Nilaparvata lugens, may provide novel tools for pest management. Here, a genome-wide survey for bHLH sequences identified 60 bHLH sequences (NlbHLHs) encoded in the draft genome of N. lugens. Phylogenetic analysis of the bHLH domains successfully classified these genes into 40 bHLH families in group A (25), B (14), C (10), D (1), E (8) and F (2). The number of NlbHLHs with introns is higher than many other insect species, and the average intron length is shorter than those of Acyrthosiphon pisum. High number of ortholog families of NlbHLHs was found suggesting functional conversation for these proteins. Compared to other insect species studied, N. lugens has the highest number of bHLH members. Furthermore, gene duplication events of SREBP, Kn(col), Tap, Delilah, Sim, Ato and Crp were found in N. lugens. In addition, a putative full set of NlbHLH genes is defined and compared with another insect species. Thus, our classification of these NlbHLH members provides a platform for further investigations of bHLH protein functions in the regulation of N. lugens, and of insects in general.

Description: Genes, Vol. 8, Pages 256: The Genetic Basis of Pericentral Retinitis Pigmentosa—A Form of Mild Retinitis Pigmentosa Genes doi: 10.3390/genes8100256 Authors: Jason Comander Carol Weigel-DiFranco Matthew Maher Emily Place Aliete Wan Shyana Harper Michael Sandberg Daniel Navarro-Gomez Eric Pierce Pericentral retinitis pigmentosa (RP) is an atypical form of RP that affects the near-peripheral retina first and tends to spare the far periphery. This study was performed to further define the genetic basis of this phenotype. We identified a cohort of 43 probands with pericentral RP based on a comprehensive analysis of their retinal phenotype. Genetic analyses of DNA samples from these patients were performed using panel-based next-generation sequencing, copy number variations, and whole exome sequencing (WES). Mutations provisionally responsible for disease were found in 19 of the 43 families (44%) analyzed. These include mutations in RHO (five patients), USH2A (four patients), and PDE6B (two patients). Of 28 putatively pathogenic alleles, 15 (54%) have been previously identified in patients with more common forms of typical RP, while the remaining 13 mutations (46%) were novel. Burden testing of WES data successfully identified HGSNAT as a cause of pericentral RP in at least two patients, suggesting it is also a relatively common cause of pericentral RP. While additional sequencing might uncover new genes specifically associated with pericentral RP, the current results suggest that genetically pericentral RP is not a separate clinical entity, but rather is part of the spectrum of mild RP phenotypes.

Description: Genes, Vol. 8, Pages 255: De Novo Assembly and Analysis of Tartary Buckwheat (Fagopyrum tataricum Garetn.) Transcriptome Discloses Key Regulators Involved in Salt-Stress Response Genes doi: 10.3390/genes8100255 Authors: Qi Wu Xue Bai Wei Zhao Dabing Xiang Yan Wan Jun Yan Liang Zou Gang Zhao Soil salinization has been a tremendous obstacle for agriculture production. The regulatory networks underlying salinity adaption in model plants have been extensively explored. However, limited understanding of the salt response mechanisms has hindered the planting and production in Fagopyrum tataricum, an economic and health-beneficial plant mainly distributing in southwest China. In this study, we performed physiological analysis and found that salt stress of 200 mM NaCl solution significantly affected the relative water content (RWC), electrolyte leakage (EL), malondialdehyde (MDA) content, peroxidase (POD) and superoxide dismutase (SOD) activities in tartary buckwheat seedlings. Further, we conducted transcriptome comparison between control and salt treatment to identify potential regulatory components involved in F. tataricum salt responses. A total of 53.15 million clean reads from control and salt-treated libraries were produced via an Illumina sequencing approach. Then we de novo assembled these reads into a transcriptome dataset containing 57,921 unigenes with N50 length of 1400 bp and total length of 44.5 Mb. A total of 36,688 unigenes could find matches in public databases. GO, KEGG and KOG classification suggested the enrichment of these unigenes in 56 sub-categories, 25 KOG, and 273 pathways, respectively. Comparison of the transcriptome expression patterns between control and salt treatment unveiled 455 differentially expressed genes (DEGs). Further, we found the genes encoding for protein kinases, phosphatases, heat shock proteins (HSPs), ATP-binding cassette (ABC) transporters, glutathione S-transferases (GSTs), abiotic-related transcription factors and circadian clock might be relevant to the salinity adaption of this species. Thus, this study offers an insight into salt tolerance mechanisms, and will serve as useful genetic information for tolerant elite breeding programs in future.

Description: Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species.

Description: Genes, Vol. 8, Pages 372: Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings Genes doi: 10.3390/genes8120372 Authors: Le Yu Jianchao Ma Zhimin Niu Xiaotao Bai Wenli Lei Xuemin Shao Ningning Chen Fangfang Zhou Dongshi Wan Salt stress is one of the most crucial factors impacting plant growth, development and reproduction. However, information regarding differences in tissue-specific gene expression patterns, which may improve a plant’s tolerance to salt stress, is limited. Here, we investigated the gene expression patterns in tissues of Populus euphratica Oliv. seedlings using RNA sequencing (RNA-Seq) technology. A total of 109.3 million, 125bp paired-end clean reads were generated, and 6428, 4797, 2335 and 3358 differentially expressed genes (DEGs) were identified in leaf, phloem, xylem and root tissues, respectively. While the tissue-specific DEGs under salt stress had diverse functions, “membrane transporter activity” was the most significant leaf function, whereas “oxidation–reduction process” was the most significant function in root tissue. Further analysis of the tissue-specific DEGs showed that the expression patterns or functions of gene families, such as SOS, NHX, GolS, GPX, APX, RBOHF and CBL, were diverse, suggesting that calcium signaling, reactive oxygen species (ROS) and salt overly sensitive (SOS) pathways are all involved in ionic homeostasis in tissues from P. euphratica seedlings. The DEGs, for example the up-regulated antioxidant genes, contribute to ROS-scavenging induced by salt stress but result in decreased Na+ concentrations in root vasculature cells and in xylem sap, while the down-regulated rbohF leads to the reverse results. These results suggest that the divergence of DEGs expression patterns contribute to maintenance of ionic and ROS homeostasis in tissues and improve plant salinity tolerance. We comprehensively analyzed the response of P. euphratica seedlings to salt stress and provide helpful genetic resources for studying plant-abiotic stress interactions.